An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution

Significance The investigation into the three-dimensional (3D) conformation of the genome has yielded crucial insights into the regulation of gene expression across both animal and plant kingdoms. Unlike animals, where genome topology is defined by topologically associating domains (TADs), plants present a comparable yet more diversified conformation across species. Addressing the unique challenge of defining TAD-like borders in plants, which lack the key architectural protein CTCF (CCCTC-binding factor), we delve into the intricate interplay between histone modifications and the 3D organization of chromatin. Our study unveils H3K9ac as a pivotal determinant, playing a major role in shaping the overall organization of chromatin in plants, providing a unique perspective on the distinctive chromatin dynamics in the absence of CTCF.


Antibodies for Immunostaining
Antibodies for ChIPseq Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.

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Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Heatmaps showing the distribution of histone modification ChIPseq signals across genes.Quantification performed according to 16 groups of expression.from low to high.Color scale represented corresponding ChIP-seq signal values.The 16 groups have been classified in the same way as in Supplementary Figure 2. The corresponding mark is indicated an the top right of each map.Supplementary Figure 4. Pie chart representing the resulting five different chromatin signatures shown in figure 1e and their corresponding gene proportion.

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Positional enrichments of 16 chromatin states relative to annotated transcription start sites (TSS) (a).transcription end sites (TES) (b) and genomic features (c).Each row represents a specific chromatin state.The color scale denotes enrichment degrees.Positive coordinate values represent the distance downstream in a 5′ to 3′ direction of transcription.while negative values represent the number of bases upstream.Distal and proximal enhancer were identified with ATAC-seq and RNA-seq data; threshold distance of 1Kb from annotated genes.Relationship between insulation index and chromatin states.(a) Heatmap presenting the insulation score values of all chromatin states.E stands for chomatin state number.The number above each chromatin state denotes their annotation as follows: A. H3K4me1 controlled genes.B. TES flanking region.C. Active regulatory elements.D. ORFs of actively transcribed genes.E. H3K4me2 repressed genes.F. Polycomb marked loci.G. Constitutive heterochromatin or intergenic region.(b) Box plot representing the median of the insulation index associated to chromatine states.X axis represents different chromatin states and y axis stands for insulation score values.which excluded outliers.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.chr8 Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.Pearson correlations for distance-normalized Hi-C interaction frequency map of chromosomes 1-12.Chromosome 3 is shown in main Figure 2. Shown above each Hi-C map from top to bottom are the following: H3K9ac signal (blue).H3K27me3 signal (red).and H3K9me2 signal (black) and PC1 (brown).For each chromosome from top left to bottom right: (a) Interactions among sequences arranged in natural order.(b) Interactions among sequences sorted by H3K9ac levels.from lowest to highest (c) Interactions among sequences sorted by H3K27me3 levels.from lowest to highest (d) Interactions among sequences sorted by H3K9me2 levels.from lowest to highest.

Table 1 .
Antibodies used for immuniostaining and ChIP-Seq analyses.

Table 2 .
Mapping statistics for hic libraries.